Commit 350bc272 authored by Thomas Schwarzl's avatar Thomas Schwarzl

added news and studies style

parent be0ced53
Pipeline #17380 passed with stage
in 1 minute and 18 seconds
CHANGES IN VERSION 0.20 alpha
-----------------------------
o Updated descriptions for studies and annotations
o Added top Mendelian disease mutation description
o Added NEWS feature
o Added FAQ
CHANGES IN VERSION 0.19 alpha
-----------------------------
o Improved table browser for RBPbase, Studies and
Annotation tabs to fit full screen browsers.
o Rearranged filtering and downloading tabs to sidebar
o added Mendelian mutation filter button
......@@ -3,7 +3,7 @@
## Thomas Schwarzl
## schwarzl@embl.de
# ----------- Global
VERSION_ = "0.1.9"
VERSION_ = "0.2.0"
VERSION_TAG_ = "alpha"
## --------- Libraries
......@@ -35,6 +35,10 @@ source("server_anno_table.R")
source("server_plots.R")
source("server_table.R")
## ---------- NEWS
NEWS <- readLines("NEWS")
## --------- Options
#options(shiny.reactlog=TRUE)
......@@ -45,7 +49,7 @@ all_organisms <- getAllOrganismsForSuperset(RIC_STUDIES)
ALLANNO <- bind_rows(ANNO_STUDIES, RIC_STUDIES)
ORGANISMS <- getOrganismSelectionList(RIC_STUDIES)
## --------- Preprossed data
## Store Preprocessed Excel table
for(i in all_organisms) {
#write.xlsx(x = COMPILED_TABLE[[i]], file = file.path(output_directory, paste0("RBPbase_", i, "_table.xlsx")))
......@@ -58,31 +62,8 @@ for(i in all_organisms) {
}
## --------- Preprossed data
jscode.autoHeightDT <- '
autoHeightDT = function() {
var offset = 100; // pixels used for other elements like title, buttons, etc
// compute the number of rows to show in window
var n = Math.floor(($(window).height() - offset) / $("#table_name tr").height());
// set the new number of rows in table
t = $("#table_name .dataTable").DataTable().page.len(n).draw();
}
// to adjust the height when the app starts, it will wait 0.8 seconds
setTimeout(autoHeightDT, 800);
// to react to changes in height of window
$(window).resize(function() {
autoHeightDT();
});
'
## --------- Graphic
cbbPalette <- c("#D55E00", "#0072B2", "#888888", "#E69F00", "#009E73", "#F0E442", "#56B4E9", "#CC79A7")
cbbPalette2 <- c("#D55E00", "#F0E442", "#0072B2", "#888888", "#E69F00", "#009E73", "#56B4E9", "#CC79A7")
mytheme <- theme_minimal() + theme(text = element_text(size = 20),
......@@ -296,7 +277,6 @@ pageMain <- fluidRow(
based protocol. The latest refinements of this protocol include enhanced RIC (eRIC) [5] and
many others which can be found under tab '<b>Studies</b>'.")),
tags$br(),
tags$br(),
tags$p(HTML("We accelerated the release of this first public version in response to the SARS-CoV-2 crisis.
We will continuously introduce refinements and welcome feedback. While no SARS-CoV-2 RNA interactome
is currently available, SARS-CoV-2 proteomics are already underway. Since SARS-CoV-2 is an RNA virus,
......@@ -304,9 +284,18 @@ pageMain <- fluidRow(
to identify relevant host proteins as RBPs, which could be helpful for understanding viral biology and
ultimately the design of therapeutic strategies. To support SARS-CoV-2 research the database also provides
<b>annotations</b> for 332 experimentally validated SARS-CoV-2-human protein-protein interactions (PPIs) [6].")),
tags$br(),
tags$p(HTML("In these early versions, RBPbase functions as a <b>table browser</b> with search,
filtering and downloading functions. We are committed
adding latest high-throughput RBP interaction studies and annotations. In near future,
RBPbase will get more sophisticated analysis and plotting functions to analyse your
RIC studies here. Stay tuned.")),
tags$br()
),
tags$div(class = "news",
verbatimTextOutput("NEWS")),
tags$br(),
tags$div(class="references",
tags$p(HTML("<b>References:</b>"), tags$br(),
"[1] Hentze, M.W., Castello, A., Schwarzl, T. and Preiss, T., 2018. A brave new world of RNA-binding proteins. Nature Reviews Molecular Cell Biology, 19(5), p.327.",
......@@ -349,17 +338,56 @@ pageInfo <- fluidRow(
"Meyerhofstraße 1", tags$br(),
"69117 Heidelberg.")),
tags$p("Please contact", tags$a(href="mailto:biohentze@embl.de", "biohentze@embl.de"),"for
support or inqueries."),
tags$br()),
support or inqueries.")),
tags$div(
tags$h1("Versions",
tags$h1("FAQ",
class = "title"),
tags$h2("Annotations and database",
tags$h2("Frequently asked questions",
class = "subtitle"),
tags$br()),
tags$div(
tags$p("The identifiers are based on Ensembl ID 92, Homology mapping was done with EggNog database[1]."),
tags$br(),
tags$div(class = "question",
tags$h4("Is the input data, code or shiny app available?"),
tags$span("All code for the backend data generation can be
found in this git repository:"),
tags$a("https://git.embl.de/schwarzl/rbpbasebackend"),
tags$span(". The shiny app and Dockerfile can be
found in this git repository: "),
tags$a("https://git.embl.de/schwarzl/rbpbase")
),
tags$div(class = "question",
tags$h4("Why summarizing by gene identifiers
and not protein identifiers?"),
tags$p("The common identifiers were individually selected
for each organism. Because protein identifiers are very
unstable, gene identifiers were used to summarize
reported RBPs. If any isoform of a protein was reported,
the gene was marked as RNA-binding.
To account for different genomic locations,
unique identifiers were created from the reported
gene names. If any of the gene identifiers was reported
to be RNA-binding, the unique identifier was marked
as RNA-binding. Genes without gene names kept their
genomic identifier."),
),
tags$div(class = "question",
tags$h4("What Ensembl versions are the identified based on?"),
tags$p("The identifiers are based on Ensembl ID version 92"),
),
tags$div(class = "question",
tags$h4("How was the homology mapping done?"),
tags$p("Homology mapping was done with EggNog database[1].
It will be revised soon."),
),
tags$div(class = "question",
tags$h4("Why is RBPbase a table browser and not a relational database?"),
tags$p("The userbase, use cases and R/Shiny specific properties prefer
precompiled tables with optional analytic or display features."),
),
tags$div(class="references",
......@@ -462,7 +490,6 @@ ui <- navbarPage(id = "menu",
tags$head(
includeHTML(file.path("www", "google-analytics.html")),
#tags$title("RBPbase"),
tags$script(jscode.autoHeightDT),
tags$link(href = "style.css", rel = "stylesheet", type = "text/css"),
useShinyjs(),
),
......@@ -506,7 +533,7 @@ ui <- navbarPage(id = "menu",
pageAnnotations
),
tabPanel(
"About",
"About / FAQ",
icon = icon("info"),
pageInfo
),
......@@ -522,6 +549,7 @@ ui <- navbarPage(id = "menu",
## --------- Server Functions
server <- function(input, output, session) {
output$NEWS <- renderText({ paste(NEWS, "\n") })
updateCurrentOrganismFilterSelection <- function(selOrganism) {
updateAwesomeCheckboxGroup(session = session,
......
......@@ -14,16 +14,18 @@ renderStudiesTable <- function(RIC_STUDIES) {
#scrollX = 400,
##fixedColumns = TRUE,
autoWidth = TRUE,
autoHeigh = TRUE,
#autoHeight = TRUE,
pageLength = nrow(RIC_STUDIES),
columnDefs = list(
list(
class = "dt-body-wrap",
targets = c(9,16,17)#,
#width = "30%"
)
)
list(
class = "dt-body-wrap",
targets = c(5, 6, 16, 17),
width = "450px"
)
)
)))
)
)
)
})
}
......@@ -5,6 +5,14 @@ html {
#RBPTableColumnSelection {
}
.question {
margin-bottom: 20px;
}
.news {
font-size: 50%;
}
.value {
text-align: center;
vertical-align: middle;
......
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